The aim of this study was to analyse the resolution power of the Next Generation Sequence (NGS) approach applied to the insight population genetics of archaeological cervid remains. Zooarchaeological studies of earth mounds of the eastern Uruguayan lowlands evidence the exploitation of several mammals including Neotropical deer. We analysed three specimens morphologically identified as pampas deer (Ozotoceros bezoarticus) dated circa 1300 years BP, recovered from the Ch2D01 archaeological site, in the San Miguel wetland of Rocha, Uruguay. We used a short fragment of the mitochondrial D-loop region and surprisingly they were determined to not correspond to pampas deer but were brown brocket deer (Mazama gouazoubira). Furthermore, the three samples contained two unique novel haplotypes. These unexpected results show the difficulty to determine these remains taxonomically by morphology, suggesting that M. gouazoubira is underestimated in the zooarchaeological record of the eastern Uruguay. This taxonomic adjustment is of great importance for the understanding of prehistoric animal economy because it involves the development of different exploitation strategies for each taxon. The results also show the usefulness of NGS to verify taxonomic identity derived from morphological analyses and its power to evaluate haplotype diversity on pooled samples from ancient DNA.